ncbi-database 开源项目推荐（44 个）

FOI-Bioinformatics /flextaxd

FlexTaxD（灵活分类数据库）——创建、添加、合并不同的分类源（QIIME、GTDB、NCBI 等）并创建宏基因组数据库（如 kraken2、ganon 等）

tlatkowski /deep-learning-gene-expression

Deep learning methods for feature selection in gene expression autism data.

Joseph7e /Assign-Taxonomy-with-BLAST

可以使用BLAST算法来分配分类标签，这种方法适用于qiime工具中。

guyleonard /taxdump_edit

🌱 ➡️ 🌳 Add new taxa or taxonomic groups to the NCBI Taxdump files

allielarocco /Microarray-Analysis

Microarray Analysis Pipeline in Python

Eldergenix /GenomeMCP

An AI-driven genomic intelligence system delivering structured ClinVar interpretation and high-precision exon, intron, and gene queries using the Model Context Protocol (MCP).

banhbio /Taxonomy.jl

Julia package to handle the NCBI Taxonomy database.

MountainMan12 /SARS-Cov2-phylo

Analysis of the viral genomes of SARS-CoV2 using MAFFT and igtree

CNuge /go-fasta

A tool for manipulating fasta files and obtaining new sequence data from NCBI in fasta format

Sarah-Hesham-2022 /BioPython-Getopt-Biological-Command-Line-Interpreter

Bio Python Project using getopt library in python and engaging with the command line prompt.

jranaraki /NCBIdataPrep

An R code to convert NCBI data files into CSV

symgenoevolab /genome_metadata

Genome Metadata Visualizer is a series of scripts written to process and visualise genome metadata after it is pulled from NCBI using the dataset and dataformat command line tools.

Jyotibrat /BotMed-Clamifision-Data-Pipeline

Data collection and curation pipeline for Clamifision, BotMed's binary medical/non-medical text classifier, aggregating and cleaning data from 10 public sources into a balanced, stratified train/val/test dataset.

erinyoung /refseq-plasmid-dl

Downloads plasmids from refseq ftp

PoorRican /ncbi-rs

Find and retrieve biological data and its metadata from NCBI

kalyaniuniversity /mgx-datasets

A list of publicly available Microarray Gene Expression datasets with proper attribution and associated toolkits.

Androidbeingx /OMIC_RESEARCH

Python class project in collab with @heloint and @AniValle. Using Entrez, Seq.io, regex, pandas

shri-path /ncbi

Crawling NCBI Pubmed Data using HTML and jQuery

ToledoEM /PubMatrixR-v2

PubMatrixR 是一个 R 软件包，利用成对组合的检索词对 PubMed 和 PMC 数据库进行系统性的文献检索。它创建共现矩阵，显示来自两个不同数据集中提及这两个术语的论文数量，使研究人员能够探索基因、疾病和通路之间的关系。

tracywong117 /NCBI-get-all-children-organism-under-ancestor

This Python script retrieve all children organism under an ancestor in NCBI taxonomy.